MEXICO CITY — More than a dozen conspirators gathered at the headquarters of the Honduran National Police just after 9:30 p.m. One of them clicked open a briefcase, and bundles of American dollars were distributed among the police officers — payment for the next day’s hit job.

After everyone else filed out of the room, the three highest-ranking officers stayed behind to make a call.

A day later, on Dec. 8, 2009, the top antidrug official in Honduras — the retired general Julián Arístides González Irías — dropped off his daughter at school and was heading to work when he found his usual route blocked. A motorcycle carrying two men pulled up to his Nissan SUV. The one riding at the back pulled out a gun, killing the general.

Outrage at the assassination swept Honduras. The country was still in turmoil after the coup that ousted President Manuel Zelaya and turned Honduras into an international outcast. In a country riddled with corruption and division, the retired general was distinguished for his rectitude and efficiency. The authorities promised a swift investigation.

But the case quickly went cold.

At least that is how it appeared to the public. Behind the scenes, according to the case files, the police investigators took just three weeks to solve the murder. The chief suspects were a cell of high-ranking police commanders working hand-in-hand with drug traffickers. The conspiracy reached all the way to the chief of police.

The man at the other end of that evening’s phone call was Winter Blanco, the head of a drug cartel based on the Caribbean coast, according to the investigators’ files. Five months earlier, the antidrug czar had foiled the trafficker’s plan to use the police to steal 143 kilograms of cocaine from a rival. The assassination was payback, investigators concluded.

Two years later, the antidrug czar’s top adviser, Alfredo Landaverde Hernández, was assassinated in exactly the same way, days after he publicly accused police commanders of allowing criminal gangs to infiltrate the police force. Once again, an investigation concluded that the chief suspects were the same commanders, aided by lower-ranking officers. A full report was sent to the police chief. But in public, the case remained unsolved.

Now, the details of the investigations — witness testimony, descriptions of videos, and phone call records — are emerging in Honduras, shaking the country once again. In terse language, the documents paint a chilling portrait of impunity at the very top of Honduras’s police hierarchy: the unchallenged power to carry out assassinations and force a cover-up of the investigation.

The suspicion that the police were part of the murders has long nagged at Hondurans. But with the release of the case files — parts of which were published in the Honduran press before being obtained by The New York Times — the country is now confronted with a glaring example of top-level government corruption and collusion with drug traffickers.

The revelations come at a pivotal time in Honduras, just as an international commission backed by the Organization of American States is setting up in the country to help investigate corruption. At the same time, the Obama administration is in the process of sending about $750 million in aid to the region, hoping to address the chronic violence and lack of opportunity that has fueled a mass exodus of desperate people to the United States.

The effort to suppress the results of two of the country’s most high-profile murder cases came to light only this month, when the newspaper El Heraldo revealed parts of the investigation’s conclusions and published excerpts from the files, without naming any of the most powerful suspects.

Since then, the Honduran president, Juan Orlando Hernández, has vowed a mass purge of the police force in response to the evidence, which helps peel back the layers covering the deeply entrenched networks of corruption feeding the country’s violence and poverty.

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Alfredo Landaverde HernándezCreditFernando Antonio/Associated Press

Last year, Oscar Chinchilla, the Honduran attorney general, asked the United States for help in solving the assassinations and Washington provided advisers, Joseph Crook, a State Department spokesman, said.

But the newly obtained case files point to a cover-up. They include cover pages from the inspector general’s office of the Security Ministry, which oversees the National Police. So if Mr. Chinchilla carries out a wide-ranging investigation to show that the government is serious about fighting corruption, it could end up ensnaring some of the president’s allies in the National Party, which has been in office since the beginning of 2010.

“There was a type of pact of silence,” said Thelma Mejía, a Honduran journalist. “These files passed through various police chiefs and they did nothing. They were known by various security ministers and they did nothing.”

The early fallout of the scandal is beginning. Foreign Minister Arturo Corrales, who had also served as the country’s security minister, resigned late Thursday. The first announcements of police firings are expected as early as this weekend. A civilian commission in charge of weeding out corrupt officers has asked for background on the nine top-ranked active generals in the police force, including José Ricardo Ramírez del Cid, a former police chief in 2011 who is named in the case files as the mastermind behind the assassinations.

According to the documents, Mr. Ramírez del Cid was one of the three who stayed behind the night before the antidrug czar was killed in 2009 to place the call to the drug lord. Another was José Luis Muñoz Licona, who was appointed police chief in 2010.

In interviews broadcast after the El Heraldo report, both officials denied any involvement in the assassinations. So did the police chief at the time of the antidrug czar’s killing, Salomón Escoto Salinas, who is also named in the documents.

The case files leave little doubt that inside the police, at least, the results of the investigation were known. In May 2012, an official in the inspector general’s office sent a copy of documents to the police chief at the time, Juan Carlos Bonilla, noting that he was acting under the orders of the security minister. At the end of 2013, Mr. Bonilla’s replacement as police chief, Ramón Sabillón Pineda, ordered special guards to protect the case files on both assassinations, as well as documents on other high-profile killings.

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Hilda Caldera, center, the widow of the assassinated antidrug official Alfredo Landaverde Hernández, was comforted during his funeral in Tegucigalpa in December 2011.CreditOrlando Sierra/Agence France-Presse — Getty Images

In remarks to the Honduran news media, four of the security ministers in office since 2009 said that they were not aware of the documents. The fifth refused to comment.

Washington will be watching the police purge closely. It spent millions of dollars on the last effort to overhaul the Honduran police, which began in 2011, before finally giving up two years later when it was clear that only a handful of officers had been fired.

“Despite good intentions, I think our own officials, especially in the past, have sometimes been naïve in the way they have supported the Honduran government’s actions and inactions,” Senator Patrick Leahy, who follows events in Honduras closely, said in written responses to questions.

Mr. Leahy, a Vermont Democrat, successfully pressed Congress to impose human rights and anticorruption conditions on aid to Central American governments this year.

“There is no doubt that our aid is well intentioned,” he wrote. “But despite some arrests of drug traffickers we’ve seen no real improvement in the Honduran justice system.” And, he promised: “It is not going to be business as usual. We can’t keep throwing money away.”

The current Honduran president, Mr. Hernández, has had his own approach to police corruption, creating a military police force that has supplanted much of the National Police force on the ground. The coming police purge is likely to strengthen its power.

The international anticorruption commission sponsored by the Organization of American States arrives this week to begin its work. Known by its Spanish initials, Maccih, it is a response to months of anticorruption protests last year across the country.

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The office of Juan Carlos Bonilla, the chief of police in 2012, was sent a copy of the documents relating to the killings.CreditOrlando Sierra/Agence France-Presse — Getty Images

The demonstrators, who marched at dusk bearing torches in a challenge to the president, demanded a prosecutors’ commission modeled after the one in neighboring Guatemala, which uncovered a customs bribery ring that brought down that country’s president last year.

Mr. Hernández resisted an accord that would create a panel with the same powers, and the commission he agreed to will not have independent investigatory authority. But the president may find that his control is limited.

In an interview, the director of the incoming group said that it would be up to his team, not the Honduran government, to choose the cases it will work on alongside Honduran prosecutors.

“There should be no doubt that the mission will be involved in cases where there are networks of corruption that harm the country,” said Juan Jiménez Mayor, the former Peruvian justice minister who is leading the commission.

Within days, the commission will start work on its first case, the assassination last month of Berta Cáceres, a prominent environmental and indigenous rights activist who was fighting a powerful Honduran company over a dam project on community land. Facing an international uproar, the government turned to the commission for help.

Even Hondurans who had been skeptical of the limits on the commission were hopeful that it will ultimately lead to widespread investigation into the police and their protectors.

“It is a special time in the country,” said Mario Díaz, a judge and president of the Association of Judges for Democracy, a group that has been critical of the Hernández government. “A lot of expectations have been generated.”

Azam Ahmed contributed reporting from Washington.

A version of this article appears in print on , on Page A6 of the New York edition with the headline: Files Suggest Police Leaders Ordered Killings of Antidrug Officials in Honduras. Order Reprints | Today’s Paper | Subscribe